[Genome] gene clusters in genome browser
Ann Zweig
ann at soe.ucsc.edu
Wed Dec 13 15:46:47 PST 2006
Hello Philippe,
You are correct, you cannot directly query a gene cluster on the Genome
Browser. You can, however, search for partial gene names and get a list of
matches. For example, search for "PCDHG" and you will see a list of hits like so:
PCDHGC3 (NM_032403) at chr5:140835753-140872730 - protocadherin gamma subfamily
C, 3 isoform 3
PCDHGC3 (NM_032402) at chr5:140835753-140838546 - protocadherin gamma subfamily
C, 3 isoform 2
PCDHGB7 (NM_032101) at chr5:140777466-140780179 - protocadherin gamma subfamily
B, 7 isoform 2
PCDHGB6 (NM_032100) at chr5:140767954-140770416 - protocadherin gamma subfamily
B, 6 isoform 2
PCDHGA11 (NM_032092) at chr5:140780721-140872730 - protocadherin gamma subfamily
A, 11 isoform 3
PCDHGA11 (NM_032091) at chr5:140780721-140783837 - protocadherin gamma subfamily
A, 11 isoform
< and so on... >
You can also type part of the gene description into the search box. For
example: "protocadherin gamma", to see a list of genes that include those words
in their description.
I know that this isn't really what you're looking for, I just wanted to point
out that you can enter partial gene names/descriptions in the search box.
We do have the gene cluster information available, it is just not searchable in
the browser. It is located in an underlying table in the hg18 database called
knownCanonical. If you are interested in querying this table to find out about
gene clusters, please write back to me with your specific needs, and I will
explain the table relationships to you.
Regards,
----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
Philippe DESSEN wrote:
> Dear colleague,
>
> It seems impossible to query gene cluster on the Genome browser ??
>
> If you refer to Entrez_Gene or HUGO , it is defined cluster of genes
> with an @.
> It would be of great interest to have directly access to the clusters
> instead to search
> for all genes inside.
>
> Is there a specific reason ?
>
> Best regards
>
> Philippe Dessen
>
>
>
> Examples actually in Entre_Gene :
>
> FAUNA@ - FAU neighboring area cluster
> HOXA@ HOX1@ homeobox A cluster
> HOXB@ HOX2@ homeobox B cluster
> HOXC@ HOX3@ homeobox C cluster
> HOXD@ HOX4@ homeobox D cluster
> IFN1@ IFNA interferon, type 1, cluster
> IFNA1 IFL;IFN;IFN-ALPHA;IFNA13;IFNA@;MGC138207;MGC138505;MGC138507
> interferon, alpha 1
> IGH@ IGH;IGH.1@;IGHDY1 immunoglobulin heavy locus
> IGHDOR15@ IGD2;IGHD/OR15;IGHDY2 immunoglobulin heavy diversity
> orphans on chromosome 15
> IGHJ@ IGHJ immunoglobulin heavy joining group
> IGHV@ IGHV immunoglobulin heavy variable group
> IGHVOR15@ IGHV;IGHV/OR15;IGHV2@;OR15 immunoglobulin heavy
> variable orphans on chromosome 15
> IGHVOR16@ IGHV;IGHV/OR16;IGHV/OR16@;IGHV3@;OR16;V(H-F)
> immunoglobulin heavy variable orphans on chromosome 16
> IGKV@ IGKV;IGKV1;IGKV1@;IGKV2;IGKV2@;IGKV3;IGKV3@ immunoglobulin
> kappa variable group
> IGKVOR2@ IGKV/OR2;IGKVP@;IGO1 Immunoglobulin kappa variable
> orphans on chromosome 2
> IGL@ IGL immunoglobulin lambda locus
> IGLC@ IGLC immunoglobulin lambda constant group
> IGLV@ IGLV immunoglobulin lambda variable group
> OLFR@ OLFR at A olfactory receptor cluster
> PGA@ - pepsinogen A gene cluster
> PR@ SPC proline-rich protein gene cluster
> RN5S1@ RN5S RNA, 5S cluster 1
> RN5S2@ - RNA, 5S cluster 2
> RN5S3@ - RNA, 5S cluster 3
> SAA@ SAA;SAA4 serum amyloid A1 cluster
> SMA@ SMA spinal muscular atrophy (Werdnig-Hoffmann disease,
> Kugelberg-Welander disease)
> TRA@
> FLJ22602;MGC117436;MGC22624;MGC23964;MGC71411;TCRA;TCRD;TRA;TRDD3
> T cell receptor alpha locus
> TRB@ TCRB;TRB T cell receptor beta locus
> TRBVOR9@ TCRBVO@;TRBV/OR9 T cell receptor beta variable
> orphans on chromosome 9
> TRD@ TCRD;TRD T cell receptor delta locus
> TRG@ TCRG;TRG T cell receptor gamma locus
> UGT1A@ GNT1;UGT;UGT1;UGT1A UDP glucuronosyltransferase 1 family,
> polypeptide A cluster
> UGT2B@ UGT2;UGT2B UDP glucuronosyltransferase 2 family,
> polypeptide B cluster
> IGKJ@ IGKJ immunoglobulin kappa joining group
> IGLJ@ IGLJ immunoglobulin lambda joining group
> IGHD@ - immunoglobulin heavy diversity group
> IGK@ IGK immunoglobulin kappa locus
> PCDHG@ PCDH2;PCDH4;PCDHG protocadherin gamma cluster
> PCDHB@ PCDH3 protocadherin beta cluster
> PCDHA@ CNR1;CNRS1 protocadherin alpha cluster
> DNM1DN1@ DNM1DN1-1;DNM1DN1-2;DNM1DN1-3;DNM1DN1-4;DNM1DN1-5
> DNM1 duplicon 1 cluster
> DNM1DN2@ DNM1DN2;DNM1DN2-1;DNM1DN2-2;DNM1DN2-3;DNM1DN2-4 DNM1
> duplicon 2 cluster
> DNM1DN3@ DNM1DN3-1;DNM1DN3-2;DNM1DN3-3;DNM1DN3-4 DNM1 duplicon 3
> cluster
> DNM1DN4@
> DNM1DN4;DNM1DN4-1;DNM1DN4-2;DNM1DN4-3;DNM1DN4-4;DNM1DN4-5 DNM1
> duplicon 4 cluster
> DNM1DN7@ DNM1DN7;DNM1DN7-1;DNM1DN7-2 DNM1 duplicon 7 cluster
> DNM1DN8@ DNM1DN8-1;DNM1DN8-2;DNM1DN8-3;DNM1DN8-4;DNM1DN8-5
> DNM1 duplicon 8 cluster
> DNM1DN9 DNM1DN9-1;DNM1DN9@ DNM1 duplicon 9
> DNM1DN10@ DNM1DN10-1;DNM1DN10-2 DNM1 duplicon 10 cluster
> DNM1DN11@
> DNM1DN11-1;DNM1DN11-10;DNM1DN11-11;DNM1DN11-12;DNM1DN11-13;DNM1DN11-14;
> DNM1DN11-2;DNM1DN11-3;DNM1DN11-4;DNM1DN11-5;DNM1DN11-6;DNM1DN11-7;
> DNM1DN11-8;DNM1DN11-9 DNM1 duplicon 11 cluster
> DNM1DN12@ DNM1DN12-1;DNM1DN12-2;DNM1DN12-3 DNM1 duplicon
> 12 cluster
> DNM1DN14@ DNM1DN14-1;DNM1DN14-2;DNM1DN14-3;DNM1DN14-4 DNM1
> duplicon 14 cluster
> DNM1DN15@ DNM1DN15-1;DNM1DN15-2;DNM1DN15-3 DNM1 duplicon
> 15 cluster
> DNM1DN16@ DNM1DN16-1;DNM1DN16-2;DNM1DN16-3 DNM1 duplicon
> 16 cluster
> DNM1DN17 DNM1DN17@ DNM1 duplicon 17
> DNM1DN5 DNM1DN5@ DNM1 duplicon 5
> SNORD113@ 14q(I) small nucleolar RNA, C/D box 113 cluster
> SNORD114@ 14q(II) small nucleolar RNA, C/D box 114 cluster
> SNORD115@ HBII-52 small nucleolar RNA, C/D box 115 cluster
> SNORD3@ U3;U3A;U3B small nucleolar RNA, C/D box 3 cluster
> SNORD116@ HBII-85 small nucleolar RNA, C/D box 116 cluster
>
>
> ------------------------------------------------------------------------
> ------------
> Philippe DESSEN Laboratoire "Génomes et Cancers" FRE
> 2939 CNRS
> Institut de Cancérologie Gustave Roussy - PR1 39 rue Camille
> Desmoulins
> 94805 VILLEJUIF Cedex - tel : 0142114490 fax : 0142116267 e-mail :
> dessenATigr.fr
> ------------------------------------------------------------------------
> ------------
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>
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